Surgical instruments go through rigorous protocols involving decontamination and sterilization. Of particular concern is Variant Creutzfeldt-Jakob Disease, because (unlike viruses and bacteria) the prions responsible for this are not destroyed by the high temperatures, cleaning chemistries, and radiation used. This paper is part of a study on the effectiveness of ultrasonically-activated streams to remove dangerous prions from surgical instruments to prevent infections from spreading between patients. Cleaning techniques are often evaluated against standard surgical instrument substitutes in a test such as animal bioassays and amplification assays. These test uses thin wires (0.016 mm diameter), which are pre-contaminated, put through the cleaning process, and then sent for analysis to determine how much contamination remains. Despite being an industry standard with proven effectiveness as a proxy for cleaning surgical instruments using heat/chemicals/radiation, thin wires are shown to be a poor proxy when ultrasonically cleaned. The acoustics of thin wires and surgical instruments differ significantly and therefore the performance of acoustic cleaning methods can fail this test while being ultimately effective on surgical instruments. We present measurements on and in the vicinity of thin wires and steel plates to illustrate the differences between these two targets and discuss the reasons for this disparity.